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A comparison of two techniques to discriminate continental origin of Atlantic salmon (Salmo salar L.) off West Greenland ArchiMer
Reddin, David; De Pontual, Helene; Prouzet, Patrick.
Two techniques of stock discrimination both utilizing scales, i. e. termed as classical technique and shape analysis, are compared for discriminating between North American and European Atlantic salmon (Salmo salar L.) caught off West Greenland. Three scales from each of 60 salmon were analyzed: 30 from North American and 30 from European-origin salmon collected from home rivers in 1982. The best results indicated misclassification and error rates of 0% for shape analysis and 5.0% and ± 1.7%, respectively, for the classical technique. A nested ANOVA indicated that variation was greater between scales of salmon of North American and European origin than from several scales from the same salmon. It was concluded that shape analysis with computer-aided...
Tipo: Text Palavras-chave: Salmo salar; Scalimétrie; Analyse de forme; Discrimination; Salmo salar; Meristics; Shape analysis; Discrimination.
Ano: 1992 URL: http://archimer.ifremer.fr/doc/00189/30073/28561.pdf
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A HMM-based model to geolocate pelagic fish from high-resolution individual temperature and depth histories: European sea bass as a case study ArchiMer
Woillez, Mathieu; Fablet, Ronan; Tran-thanh Ngo,; Lalire, Maxime; Lazure, Pascal; De Pontual, Helene.
Numerous methods have been developed to geolocate fish from data storage tags. Whereas demersal species have been tracked using tide-driven geolocation models, pelagic species which undertake extensive migrations have been mainly tracked using light-based models. Here, we present a new HMM-based model that infers pelagic fish positions from the sole use of high-resolution temperature and depth histories. A key contribution of our framework lies in model parameter inference (diffusion coefficient and noise parameters with respect to the reference geophysical fields—satellite SST and temperatures derived from the MARS3D hydrodynamic model), which improves model robustness. As a case study, we consider long time series of data storage tags (DSTs) deployed on...
Tipo: Text Palavras-chave: Fish movement; Archival tagging; Migration; Population structure; Hidden Markov Model (HMM); State-space model.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00300/41097/40270.pdf
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A review of image-based tools for automatic fish ageing from otolith features ArchiMer
Carbini, Sebastien; Chessel, Anatole; Benzinou, Abdesslam; Fablet, Ronan; Mahe, Kelig; De Pontual, Helene.
Most of European fish stocks are assessed using age-based models, and otolith interpretation for age estimations costs several million euros annually. In this context, automated ageing systems would provide a mean to 1) standardize ageing, 2) control ageing consistency within and between ageing laboratories 3) build interpreted image data bases ensuring the information conservation and sharing and 4) improve growth studies while reducing the cost of the acquisition of age data. This paper presents a review of different image-based tools for automatic fish ageing from otolith features within the framework of AFISA (EU STREP project on Automated FISh Ageing coordinated by Ifremer). The full automatic ageing process can be divided into three main steps: 1)...
Tipo: Text
Ano: 2008 URL: http://archimer.ifremer.fr/doc/00024/13519/10546.pdf
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Aide à l'estimation des stocks d'huîtres en élevage par télédétection basse altitude: étude de faisabilité ArchiMer
De Pontual, Helene.
Existing methods to assess the biomass of reared oyster's stocks are ail based on aerial photographs and field data. In this study, we propose an automatic processing of the digitized aerial photographs making use of advanced vision tools such as mathematical morphology. The implemented a1gorithms are described. They give enough convincing results to suggest further developments. However, this method requires the use of digital images. To this respect, a part of this paper deals with data acquisition problems. We particularly study the feasibility of using airborne video recording system. Such device should give a quite accurate information, easier to process than the classical aerial photographs.
Tipo: Text Palavras-chave: Huître; Estimation des stocks; Photographie aérienne; Vidéo aéroportée; Analyse d'images numériques; Oysters; Stock assessment; Aerial pholographs; Airborne videography; Digital image processing.
Ano: 1989 URL: http://archimer.ifremer.fr/doc/00105/21669/19247.pdf
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Are hake otolith macrostructures randomly deposited? Insights from an unsupervised statistical and quantitative approach applied to Mediterranean hake otoliths ArchiMer
Courbin, Nicolas; Fablet, Ronan; Mellon-duval, Capucine; De Pontual, Helene.
Individual fish age data are crucial to fish stock assessment, so their accuracy and precision are vital. The acquisition of age data most often relies on interpreting fish otoliths, a complex task in which expert subjectivity increases with the complexity of the structural patterns of the otoliths. The question arises for certain fish species (e.g. hake, Merluccius merluccius) whether the deposition of otolith macrostructures is meaningful for age estimation. A quantitative method based on the evaluation of otolith similarity in terms of structural patterns is presented to investigate this issue. It relies on the determination of a typology of otolith macrostructures from an unsupervised statistical analysis of the distributions of their characteristics....
Tipo: Text Palavras-chave: Quality control; Otolith; Merluccius merluccius; Growth; Age estimation method; Age.
Ano: 2007 URL: http://archimer.ifremer.fr/doc/2007/publication-2678.pdf
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Automatic Fish Ageing (AFISA) ArchiMer
Mahe, Kelig; Parisi, Vincenc; Carbini, Sebastien; Soria, J.a.; Harbitz, A; De Pontual, Helene; Cotano, U; Songer, S; Millner, R; Lewy, P; Gudmundsson, E.f; Fablet, Ronan; Benzinou, Abdesslam.
Most of the fish stocks are assessed using age-based models, however age estimations using otoliths costs several million euros annually. In this context, Automatic Fish Ageing (EU Project) would provide means to standardize ageing among laboratories and build interpreted image databases ensuring the information conservation. Automation improves growth studies while reducing the cost of the acquisition of age data. The whole processing chain from the acquisition of otolith data to the actual ageing issue using pattern recognition or statistical inference has been realised for three case studies : a) Cod (Gadus morhua ; Faeroes, North Sea, North East Arctic) b) Anchovy (Engraulis encrasicolus ; Bay of Biscay) c) Plaice (Pleuronectes platessa, Eastern...
Tipo: Text
Ano: 2009 URL: http://archimer.ifremer.fr/doc/00011/12270/10548.pdf
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Bar commun ArchiMer
De Pontual, Helene; Drogou, Mickael.
Tipo: Text
Ano: 2018 URL: http://archimer.ifremer.fr/doc/00444/55575/57188.pdf
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Characterization and variations of organic parameters in teleost fish endolymph during day-night cycle, starvation and stress conditions ArchiMer
Guibbolini, M; Borelli, G; Mayer Gostan, N; Priouzeau, F; De Pontual, Helene; Allemand, D; Payan, P.
The aim of the present work was to examine the modifications of the organic composition of fish endolymph under environmental conditions (day-night cycle, starvation and Cl-2-Stress) known to modify otolith growth. Endolymph electrophoretic patterns were compared. An antibody raised against the trout otolith organic matrix allowed examining the variations of organic matrix precursors in the endolymph under the above conditions. Western blot analysis showed bands around 60-80 kDa. A 50% decrease of immunolabelling was observed during the night whereas increases were seen after starvation (factor 3) or stress (factor 2) suggesting that these variations could be related to the organic matrix deposit. A factor retarding in vitro CaCO3 crystallization (FRC) was...
Tipo: Text Palavras-chave: Turbot; Trout; Stress; Starvation; Day night cycle; Organic matrix; Otolith calcification; In vitro crystallization; Endolymph.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1875.pdf
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Comparison of 0- and 2-group otolith elemental signatures to discriminate Solea solea nurseries in the bay of biscay ArchiMer
Durieux, Eric D. H.; Labonne, Maylis; Begout, Marie-laure; De Pontual, Helene.
The common sole Solea solea (L.) is a commercially important and widely distributed flatfish of the North-East Atlantic. For the Bay of Biscay stock, sole nurseries display differences in terms of quantity and quality. In fine the measure of the quality of a habitat for juveniles of a particular species is expressed by the contribution to the recruitment into the adult population. Understanding this connectivity between juvenile and adult habitats, i.e. evaluating the contribution of each nursery to a single adult stock appears essential in terms of stock management. However, this critical link is still missing for the Bay of Biscay sole stock. Determining if nurseries could be discriminated using otolith elemental composition analysis constitutes the...
Tipo: Text
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00073/18377/15949.pdf
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Consequences of bias in age estimation on assessment of the northern stock of European hake (Merluccius merluccius) and on management advice ArchiMer
Bertignac, Michel; De Pontual, Helene.
The results of a pilot tagging study on hake (Merluccius merluccius), conducted in the northern part of the Bay of Biscay in 2002, indicate that growth rates for this stock may be currently underestimated because of biased estimates of age. The impact that such a bias may have on the stock dynamics and the trends of the key population parameters, recruitment, spawning-stock biomass (SSB), and mortality are investigated. Assuming new growth parameters, a new age-length key is derived and used to produce and catch-at-age data and abundance indices, which are then used to assess the stock. Bias in estimating age affects the absolute levels of fishing mortality and stock biomass estimates, and also impacts the trend in SSB. However, trends in fishing mortality...
Tipo: Text Palavras-chave: Tagging; Stock assessment; Simulation; Management; Growth; European hake; Age estimation.
Ano: 2007 URL: http://archimer.ifremer.fr/doc/2007/publication-2824.pdf
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Contribution of a bioenergetics model to investigate the growth and survival of European seabass in the Bay of Biscay – English Channel area ArchiMer
Dambrine, Chloe; Huret, Martin; Woillez, Mathieu; Pecquerie, Laure; Allal, Francois; Servili, Arianna; De Pontual, Helene.
The European seabass (Dicentrarchus labrax) is a species of particular ecological and economic importance. Stock assessments have recently revealed the worrying state of the “Northern stock”, probably due to overfishing and a series of poor recruitments. The extent to which these poor recruitments are due to environmental variability is difficult to assess, as the processes driving the seabass life cycle are poorly known. Here we investigate how food availability and temperature may affect the growth and survival of wild seabass at the individual scale. To this end, we developed a bioenergetics model based on the Dynamic Energy Budget (DEB) theory. We applied it to seabass population of the Northeast Atlantic region (Bay of Biscay – English Channel area)...
Tipo: Text Palavras-chave: Dicentrarchus labrax Northeast Atlantic Dynamic Energy Budget theory Growth; Starvation Early-life stages.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00612/72397/71341.pdf
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Coupling spectral analysis and hidden Markov models for the segmentation of behavioural patterns ArchiMer
Heerah, Karine; Woillez, Mathieu; Fablet, Ronan; Garren, Francois; Martin, Stephane; De Pontual, Helene.
Background Movement pattern variations are reflective of behavioural switches, likely associated with different life history traits in response to the animals’ abiotic and biotic environment. Detecting these can provide rich information on the underlying processes driving animal movement patterns. However, extracting these signals from movement time series, requires tools that objectively extract, describe and quantify these behaviours. The inference of behavioural modes from movement patterns has been mainly addressed through hidden Markov models. Until now, the metrics implemented in these models did not allow to characterize cyclic patterns directly from the raw time series. To address these challenges, we developed an approach to i) extract new metrics...
Tipo: Text Palavras-chave: Fourier transform; Non negative matrix factorization; Classification; Animal behaviour; European sea bass; Movement ecology; Diurnal and tidal cycles; Biologging; Data storage tags.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00402/51400/51974.pdf
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Daily variations of endolymph composition: relationship with the otolith calcification process in trout ArchiMer
Borelli, G; Guibbohni, M; Mayer Gostan, N; Priouzeau, France; De Pontual, Helene; Allemand, D; Puverel, S; Tambutte, E; Payan, P.
Ionic and organic parameters of the otolith calcification process in the trout Oncorhynchus mykiss were analysed in plasma and endolymph over the day:night cycle. Plasma pH remained constant and total CO2 concentration was significantly lower (by 21%) during the day than at night. Calcifying parameters (total CO2, total calcium concentration) were measured in the proximal and distal endolymphs and were unchanged in the latter during the day:night cycle, but fluctuated in the former. Non-collagenous protein and collagen concentrations in endolymph were higher (1.5- and 10-fold, respectively) during the day than at night. As there was no change in total calcium concentration, we propose that Ca2+ increases during the dark period and was maximal by the end of...
Tipo: Text Palavras-chave: Endolymph; Day night cycle; Calcification; Otolith.
Ano: 2003 URL: https://archimer.ifremer.fr/doc/2003/publication-418.pdf
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Daily variations of the saccular endolymph and plasma compositions in the turbot Psetta maxima: relationship with the diurnal rhythm in otolith formation ArchiMer
Edeyer, Anaick; De Pontual, Helene; Payan, P; Troadec, Herve; Severe, Armelle; Mayer-gostan, N.
We studied the circadian variations of the ionic composition ([Na+], [K+], [Cl-]), total CO2 ([tot CO2]), and protein concentration ([protein]) in the plasma and endolymph in the distal and proximal sides of the sacculus in the turbot Psetta maxima. Daily variations in total plasma calcium ([tot Ga]) were also recorded. Significant diurnal fluctuations occurred in most parameters and the spatial heterogeneity of the endolymph composition was maintained throughout a 24 h period. The main parameters implicated in otolith calcification, endolymph [tot CO2] and endolymph [protein], fluctuated diurnally, [tot CO2] was highest and [protein] lowest at night; the relative concentrations were reversed during the day. The inverse, alternating relationship of maximal...
Tipo: Text Palavras-chave: Daily cycle; Endolymph; Otolith; Chemical composition; Teleost.
Ano: 2000 URL: http://archimer.ifremer.fr/doc/00000/10572/7603.pdf
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Diet is correlated with otolith shape in marine fish ArchiMer
Mille, Tiphaine; Mahe, Kelig; Cachera, Marie; Villanueva, Ching-maria; De Pontual, Helene; Ernande, Bruno.
Previous studies have shown that food amount influence fish otolith structure, opacity and shape and that diet composition has an effect on otolith chemical composition. This study investigated the potential correlation between diet and otolith shape in 5 wild marine fish species by addressing 4 complementary questions. First, is there a global relationship between diet and otolith shape? Second, which prey categories are involved in this relationship? Third, what are the respective contributions of food quantity and relative composition to diet–otolith shape co-variation? Fourth, is diet energetic composition related to otolith shape? For each species, we investigated how otolith shape varies with diet. These questions were tackled by describing diet in...
Tipo: Text Palavras-chave: Fourier analysis; English Channel; Interspecific; Morphometric analysis; Otolith growth; Saccular otolith; Stomach contents.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00345/45639/45269.pdf
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Directional bilateral asymmetry in otolith morphology may affect fish stock discrimination based on otolith shape analysis ArchiMer
Mahe, Kelig; Ider, Djamila; Massaro, Andrea; Hamed, Oussama; Jurado-ruzafa, Alba; Goncalves, Patricia; Anastasopoulou, Aiketerini; Jadaud, Angelique; Mytilineou, Chryssi; Elleboode, Romain; Ramdane, Zohir; Bacha, Mahmoud; Amara, Rachid; De Pontual, Helene; Ernande, Bruno.
Otolith shape analysis is an efficient fish stock identification tool. However, most applications used left and right otoliths or only one of them arbitrarily chosen without testing for biases resulting from potential directional bilateral asymmetry (DA) in otolith shape, i.e. a unimodal population-level deviation form bilateral symmetry between right and left otolith shapes. In this study, 560 bogues (Boops boops) were sampled from 11 geographical locations from the Canary Islands to the Aegean Sea and elliptical Fourier descriptors were used to describe their otoliths’ shape. First, a significant otolith DA was observed at the global scale with an average amplitude of 2.77%. However, at the scale of sampling locations, DA was not always significant and...
Tipo: Text Palavras-chave: Boops boops; Elliptical Fourier analysis; Mediterranean Sea; Side effect; Stock identification.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00468/57967/60418.pdf
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Effects of T-bar and DST Tagging on Survival and Growth of European Hake ArchiMer
Jolivet, Aurelie; De Pontual, Helene; Garren, Francois; Begout, Marie-laure.
Controlled experiments were conducted to assess the effects of T-bar and DST tagging on post-release survival and growth of European hake. In this study, two groups of each 30 hake were considered: small fish (SF, average total length: 29.9 cm +/- 2.2 cm) and large fish (LF, average total length: 36.4 cm +/- 2.5 cm). Within each size group, fish were randomly assigned to one of 3 treatment groups: control (C), T-bar tagging referred as conventional tagging (CT) and DST tagging (DST) with dummy tags. After 4 months, the overall survival rate was 35%. Smaller fish were less impacted by the stress induced by handling, anaesthesia and tagging and in the SF group, the survival rates were similar (30%) for CT or DST. Specific growth rates were highly variable...
Tipo: Text Palavras-chave: Merluccius merluccius; Archival tag; Husbandry; Midterm experiment; Captive hake.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/00065/17645/15196.pdf
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Elaboration d'un plan de gestion du bar ArchiMer
Drogou, Mickael; Biseau, Alain; Berthou, Patrick; De Pontual, Helene; Habasque, Jeremie; Le Grand, Christelle; Pitel-roudaut, Mathilde.
Tipo: Text
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00049/16007/14661.pdf
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Evidence of underestimation of European hake growth in the Bay of Biscay, and its relationship with bias in the agreed method of age estimation ArchiMer
De Pontual, Helene; Groison, Anne-laure; Pineiro, Carmen; Bertignac, Michel.
In 2002, a pilot experiment on hake tagging was carried out using methodology specifically developed to catch and handle fish in,good condition. By the end of 2005, 36 hake and five tags had been returned to the laboratory (a 3.1% return rate) with a maximum time at liberty of 1066 days. The somatic growth of the recoveries proved to be twofold higher than that expected from published von Bertalanffy growth functions for the species in the Bay of Biscay. The growth underestimation was related to age overestimation, as demonstrated by two independent analyses. The first was based on a blind interpretation of marked otoliths conducted independently by two European experts involved in the routine age estimation of hake. The result shows that the age estimates...
Tipo: Text Palavras-chave: Tagging; Otolith; Merluccius merluccius; Growth; European hake; Age validation; Age estimation method; Age.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-2221.pdf
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Gadoids ArchiMer
Hussy, Karin; Morales-nin, Beatriz; Pineiro Alvarez, Carmen; De Pontual, Helene; Smith, Joanne; Mahe, Kelig; Krumme, Uwe; Songer, Sally; Walther, Yvonne; Rey, Javier.
This chapter was written during the Workshop on Age Validation of Gadoids (WKAVGS 2013) which was held 6–10 May 2013 at Imedea in Esporles, Mallorca. The terms of reference for the workshop were to: 1. Review information on age estimations, otolith exchanges, workshops, and validation works done so far on the following species: European hake, cod, pollock, saithe, haddock, whiting, and blue whiting; 2. Assemble and compare the results of different validation methods (i.e. marking and recapture, marking the calcified structure, marginal increment analysis, marginal analysis, modal progression analysis, length back-calculation, etc.); 3. Discuss and propose the most appropriate validation methods of age and growth pattern of calcified structures (CS), for...
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00620/73189/72379.pdf
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